Mercurial > repos > artbio > repenrich2
diff edger-repenrich2.xml @ 1:6d59fbca2db4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 4dd520dee5c3c0c526e8319a74c4890da032300f
| author | artbio |
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| date | Sat, 20 Apr 2024 14:46:12 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/edger-repenrich2.xml Sat Apr 20 14:46:12 2024 +0000 @@ -0,0 +1,199 @@ +<tool id="edger-repenrich2" name="edgeR-repenrich2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Determines differentially expressed features from RepEnrich2 counts</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edgeR_requirements"/> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occurred, please check your input carefully and contact your administrator." /> + </stdio> + <version_command> + <![CDATA[ + echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR) && + cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]> + </version_command> + <command> + <![CDATA[ + #import json + Rscript '${__tool_directory__}/edgeR_repenrich2.R' + --factorName '$factorName' + + --levelNameA '$factorLevel_A' + #set $factorlevelsA = list() + #for $file in $countsFiles_A: + $factorlevelsA.append(str($file)) + #end for + $factorlevelsA.reverse() + --levelAfiles '#echo json.dumps(factorlevelsA)#' + + --levelNameB '$factorLevel_B' + #set $factorlevelsB = list() + #for $file in $countsFiles_B: + $factorlevelsB.append(str($file)) + #end for + $factorlevelsB.reverse() + --levelBfiles '#echo json.dumps(factorlevelsB)#' + + -o 'edger_out' + + -p '$plots' + #if $normCounts: + -n '$counts_out' + #end if + -o '$edger_out' + ]]> + </command> + <inputs> + <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. genotype or age or drug_x" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="factorLevel_A" type="text" value="FactorLevel1" label="Specify a factor level, typical values could be 'mutant' or 'Drug_X'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="countsFiles_A" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich" /> + <param name="factorLevel_B" type="text" value="FactorLevel2" label="Specify a factor level, typical values could be 'wildtype' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="countsFiles_B" type="data" format="tabular" multiple="true" label="Counts file(s)" help="Count files must have been generated by repenrich tool" /> + <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="Output normalized counts table" /> + </inputs> + <outputs> + <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}"> + <actions> + <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" /> + </actions> + </data> + <data format="pdf" name="plots" label="edgeR plots" /> + <data format="tabular" name="counts_out" label="Normalized counts file"> + <filter>normCounts == True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="factorName" value="Genotype"/> + <param name="factorLevel_A" value="Mutant"/> + <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> + <param name="factorLevel_B" value="Wildtype"/> + <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/> + <param name="normCounts" value="True"/> + <output name="counts_out" file="Normalized_counts_file.tab"/> + <output name="plots" file="edgeR_plots.pdf"/> + <output name="edger_out" file="edgeR_result_file.tab"/> + + </test> + </tests> + <help> +<![CDATA[ +.. class:: infomark + +**What it does** + +Estimate Distance between samples (MDS) and Biological Coefficient Variation (BCV) in count +data from high-throughput sequencing assays and test for differential expression using edgeR_. + +**Inputs** + +edger-repenrich takes count tables generated by repenrich as inputs. A repenrich count table looks +like: + +============== ========== ========== ========== +LSU-rRNA_Dme rRNA rRNA 3659329 +-------------- ---------- ---------- ---------- +FW3_DM LINE Jockey 831 +-------------- ---------- ---------- ---------- +DMTOM1_LTR LTR Gypsy 1004 +-------------- ---------- ---------- ---------- +R1_DM LINE R1 7343 +-------------- ---------- ---------- ---------- +TAHRE LINE Jockey 4560 +-------------- ---------- ---------- ---------- +G4_DM LINE Jockey 3668 +-------------- ---------- ---------- ---------- +BS LINE Jockey 7296 +-------------- ---------- ---------- ---------- +Stalker2_I-int LTR Gypsy 12252 +-------------- ---------- ---------- ---------- +Stalker3_LTR LTR Gypsy 593 +-------------- ---------- ---------- ---------- +TABOR_I-int LTR Gypsy 3947 +-------------- ---------- ---------- ---------- +G7_DM LINE Jockey 162 +-------------- ---------- ---------- ---------- +BEL_I-int LTR Pao 23757 +-------------- ---------- ---------- ---------- +Gypsy6_I-int LTR Gypsy 7489 +============== ========== ========== ========== + +Count tables must be generated for each sample individually. Here, edgeR_ is handling a +single factor (genotype, age, treatment, etc) that effect your experiment. This factor has +two levels/states (for instance, "wild-type" and "mutant". You need to select appropriate +count table from your history for each factor level. + +The following table gives some examples of factors and their levels: + +========= ============== =============== +Factor Factorlevel1 Factorlevel2 +--------- -------------- --------------- +Treatment Treated Untreated +--------- -------------- --------------- +Genotype Knockdown Wildtype +--------- -------------- --------------- +TimePoint Day4 Day1 +--------- -------------- --------------- +Gender Female Male +========= ============== =============== + +*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. +Here the order of factor levels is important. For example, for the factor 'Treatment' given +in above table, edgeR computes fold changes of 'Treated' samples against 'Untreated', +i.e. the values correspond to up or down regulations of genes in Treated samples. + +**Output** + +edgeR_ generates a tabular file containing the different columns and results visualized in +a PDF: + +====== ============================================================================= +Column Description +------ ----------------------------------------------------------------------------- + 1 Tag (transposon element ID) + 2 the logarithm (to basis 2) of the fold change (See the note in inputs section) + 3 p value adjusted for multiple testing with the Benjamini-Hochberg procedure + which controls false discovery rate (FDR) + 4 Class the transposon belongs to + 5 Type the transposon belongs to +====== ============================================================================= + +.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html +]]> + +**Note**: This edgeR_ wrapper was adapted from code available at +https://github.com/nskvir/RepEnrich + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp616</citation> + </citations> +</tool>